Tunnel junctions in microfluidic arrays for molecular recognition

ABSTRACT

Embodiments of the present technology include a system for analyzing a molecule. The system may include a device. The device includes a first conductive element, a second conductive element, and an insulating layer. The insulating layer may be tapered in a direction to reach a minimum thickness at a first end of the device. The insulating layer is disposed between the first conductive element and the second conductive element. The device may include a voltage source in electrical communication with the first conductive element and the second conductive element. The device may also include an electrical meter in electrical communication with the voltage source, the first conductive element, and the second conductive element.

CROSS-REFERENCES TO RELATED APPLICATIONS

This application claims priority to U.S. Provisional Application No.62/369,704, filed Aug. 1, 2016, which is incorporated herein byreference in its entirety for all purposes.

FIELD

This application relates to methods and systems to analyze moleculesusing tunnel junctions. Such analysis of molecules can includesequencing biological polymers, such as nucleic acids.

BACKGROUND

Possible technologies for analyzing single molecules (e.g. nucleicacids) include tunneling junction devices that have a sub-molecularsized gap between two electrodes. When the molecule makes contact withthe two electrode, the molecule may create a tunneling current. Thetunneling current can be analyzed to identify a portion of the molecule.Dimensions of the gap may be on the order of nanometers, including lessthan 2 nm, or even sub-nanometer. Creating a gap of this size mayrequire precise and expensive techniques. Toolsets and processes fortunnel junctions have been developed by magnetic recording mediaindustry to manufacture magnetic junctions for hard-drives andnon-volatile memory devices that are currently under development (W.Zhao, et al., “Failure Analysis in Magnetic Tunnel Junction Nanopillarwith Interfacial Perpendicular Magnetic Anisotropy,” Materials, Vol. 9,41, 2016; P. Tyagi, E. Friebe, and C. Baker, “Advantages ofPrefabricated Tunnel Junction-Based Spintronic s Devices,” NANO: BriefReports and Reviews, Vol. 10, 1530002, 2015).

Devices with such a small gap between electrodes may be subject todevice failure, such as electrical shorts. Furthermore, maintaining sucha thin layer between two electrodes is difficult. Improvements in thedesign and manufacturability of tunneling junction devices are stillneeded, particularly for analyzing single molecules. Ideally, design andmanufacturability improvements should not come at the expense ofaccurate and precise analysis. These and other issues are addressed bythe technology described in this document.

BRIEF SUMMARY

Embodiments of the present technology may allow for the analysis ofmolecules (e.g., sequencing of nucleic acid molecules) by tunnelingrecognition at a tunneling junction. A tunneling junction of the presenttechnology can include an insulating layer between two electrodes. Avoltage may be applied to the electrodes. When a molecule makes contactwith both electrodes, the molecule allows current to tunnel through themolecule. The characteristics of the current may aid in identifying aportion of the molecule, for example, a particular nucleotide or basepresent in a nucleic acid molecule.

Embodiments of the present technology may also allow for repeatedtunneling current measurements or other electrical characteristicmeasurements of molecules across multiple tunneling junctions. Thecontact point of the electrodes with the molecule can be oriented sothat the molecule can move to another tunneling junction device and makecontact with the electrodes of that device. The tunneling direction maythen be parallel with the substrate instead of orthogonal to thesubstrate. In this orientation, an electric field or a pressure gradientacross the substrate can move molecules to be analyzed from onetunneling junction to another tunneling junction. A molecule can thenmake contact with multiple tunneling junctions, including hundreds,thousands, or tens of thousands of tunneling junctions. As a result,better statistics can be developed to identify the molecule or a portionof the molecule.

In some embodiments, the insulating layer may be tapered so that theminimum thickness is the closest part of the insulating layer to themolecule when the molecule contacts the electrodes. The minimumthickness may be on the order of nanometers or even sub-nanometer. Byhaving an increased thickness at other portions of the insulating layer,the current or other electrical characteristic signature from themolecule can be easier to detect, as fewer electrons will tunnel throughthicker portions of the insulating layer. In addition, thicker portionsof the insulating layer may be less likely to have defects or allowelectrical shorts. Furthermore, a tapered insulating layer may also beeasier to manufacture than an insulating layer having a uniformthickness on the nanometer scale.

In some embodiments, tunneling junction devices may be oriented to forma flow channel such that a molecule may flow through the flow channel asa substantially linear or uncoiled molecule. A molecule may flow againstthe electrode of a first tunneling junction device and then move towardthe electrode of a second tunneling junction device. The orientation ofthese devices forces the molecule to move in a way that prevents themolecule from coiling and allows for the molecule to contact multipledevices and register a tunneling current or other electricalcharacteristic with each device.

A better understanding of the nature and advantages of embodiments ofthe present invention may be gained with reference to the followingdetailed description and the accompanying drawings.

Definitions

The term “contacting” may refer to bringing one object in proximity toanother object such that electrons may tunnel from one object throughthe other object. At a subatomic level, two objects may never physicallytouch each other as repulsive forces from electron clouds in the objectsmay prevent the objects from coming into closer proximity.

“Nucleic acid” may refer to deoxyribonucleotides or ribonucleotides andpolymers thereof in either single- or double-stranded form. The term mayencompass nucleic acids containing known nucleotide analogs or modifiedbackbone residues or linkages, which are synthetic, naturally occurring,and non-naturally occurring, which have similar binding properties asthe reference nucleic acid, and which are metabolized in a mannersimilar to the reference nucleotides. Examples of such analogs mayinclude, without limitation, phosphorothioates, phosphoramidites, methylphosphonates, chiral-methyl phosphonates, 2-O-methyl ribonucleotides,peptide-nucleic acids (PNAs).

Unless otherwise indicated, a particular nucleic acid sequence alsoimplicitly encompasses conservatively modified variants thereof (e.g.,degenerate codon substitutions) and complementary sequences, as well asthe sequence explicitly indicated. Specifically, degenerate codonsubstitutions may be achieved by generating sequences in which the thirdposition of one or more selected (or all) codons is substituted withmixed-base and/or deoxyinosine residues (Batzer et al., Nucleic AcidRes. 19:5081 (1991); Ohtsuka et al., J. Biol. Chem. 260:2605-2608(1985); Rossolini et al., Mol. Cell. Probes 8:91-98 (1994)). The termnucleic acid is used interchangeably with gene, cDNA, mRNA,oligonucleotide, and polynucleotide.

The term “nucleotide,” in addition to referring to the naturallyoccurring ribonucleotide or deoxyribonucleotide monomers, may beunderstood to refer to related structural variants thereof, includingderivatives and analogs, that are functionally equivalent with respectto the particular context in which the nucleotide is being used (e.g.,hybridization to a complementary base), unless the context clearlyindicates otherwise.

The term “electrical characteristic” may be understood to refer to anyproperty related to an electrical circuit. Electrical characteristic mayrefer to voltage, current, resistance, impedance, inductance, orcapacitance, and time variations thereof (e.g., current frequency).

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 shows a system of conventional vertical tunnel junctions.

FIG. 2 shows a system of tunneling junctions according to embodiments ofthe present technology.

FIG. 3A shows a system of tunneling junctions that are laterally taperedaccording to embodiments of the present technology.

FIG. 3B shows a system of tunneling junctions that are verticallytapered according to embodiments of the present technology.

FIG. 4A and FIG. 4B show views of a tunneling junction without a taperaccording to embodiments of the present technology.

FIG. 5 shows a system of laterally tapered tunneling junctions accordingto embodiments of the present technology.

FIG. 6 shows a method of analyzing a molecule according to embodimentsof the present technology.

FIG. 7 shows a method of manufacturing a device for analyzing a moleculeaccording to embodiments of the present technology.

FIG. 8A and FIG. 8B show an example method of manufacturing verticallytapered tunneling junction devices according to embodiments of thepresent technology.

FIG. 9A and FIG. 9B show an example method of manufacturing laterallytapered tunneling junction devices according to embodiments of thepresent technology.

FIG. 10 shows a computer system according to embodiments of the presenttechnology.

FIG. 11 shows an analysis system according to embodiments of the presenttechnology.

FIG. 12 shows a computer system according to embodiments of the presenttechnology.

DETAILED DESCRIPTION

Conventional tunneling junction devices used commercially in themagnetic recording media industry are not suitable for tunnelingrecognition analysis of molecules, including nucleic acids and otherbiological polymers. Biological polymers may include DNA, RNA, cDNA,mRNA, oligonucleotide, polynucleotide, amino acids, proteins,polypeptides, carbohydrates, and/or lipids. Conventional tunnelingjunction devices in the magnetic recording media industry may also notbe suitable for tunneling recognition because the tunneling junctionsare not oriented to allow for repeated contact with and measurements ofa molecule.

I. Tunneling Junctions in Magnetic Media Industry

FIG. 1 shows a system 100 of conventional tunneling junction devicesused commercially in the magnetic media industry. A device is fabricatedon an insulating substrate 102. The device includes a first metal layer104. An insulating layer 106 is on top of first metal layer 104. Asecond metal layer 108 is on top of insulating layer 106. Thisconfiguration may be convenient to fabricate, but the configuration isnot ideal for analyzing molecules.

To generate a tunneling current, a molecule would have to contact thefirst metal layer 104 and the second metal layer 108, which are stackedvertically. As a result, the tunneling direction is vertical, as viewedin FIG. 1. The molecule, traveling along the tunneling direction, wouldcontact only a single device and not contact multiple devices. Hence, amolecule may generate only one current measurement in FIG. 1, ratherthan multiple current measurements. The current measurements may benoisy because the magnitude of the current measurement may be on theorder of tens to hundreds of picoamps and because the molecule may notadequately contact the devices at all portions of interest (e.g., forevery nucleotide of a nucleic acid). Increasing the number ofmeasurements for a molecule will help provide more greater accuracy foranalyzing the molecule, but FIG. 1 cannot consistently providerepeatable measurements of a molecule. As a result, these conventionaltunneling junction devices may not allow for an accurate and reliablemethod for analyzing nucleic acids or other molecules.

II. Orientation and Tapering of Tunneling Junction Device

FIG. 2 shows a system 200 of tunneling junction devices according toembodiments of the present technology. An insulating layer 202 isbetween a first metal layer 204 and a second metal layer 206. UnlikeFIG. 1, all three layers are in contact with an insulating substrate208. As a result, the tunneling direction is horizontal, as viewed inFIG. 2. With a horizontal tunneling direction, a molecule can contactmultiple devices 210, 212, 214, and 216 along insulating substrate 208.

The tunneling junction may be oriented such that the side contacting themolecule to be analyzed is on the side of the device opposite theinsulating structure (e.g., in FIG. 2, toward the top of the figure).With this orientation, the path of a molecule that moves from left toright in FIG. 2 along the tops of the devices 210, 212, 214, and 216 maygenerate a tunneling current in the multiple devices. This possible pathof a molecule along the tops of the devices in FIG. 2 is shown by thedotted arrow 218. A current meter 222 is shown, but current meter 222may be a voltage meter or any other electrical meter. Similarly, anycurrent meter shown in any of the figures may be a voltage meter orother electrical meter. The tops of the devices may be substantiallyplanar. For example, the tops of the devices may not form part of acurved surface of a cylinder, such as that in a nanopore tunneljunction.

In other embodiments, the tunneling junction may be oriented such thatthe side contacting the molecule is on the side of the device that isorthogonal to the insulating substrate (e.g., in FIG. 2, the side facingthe viewer of the figure). With this orientation, the path of a moleculethat moves left to right in FIG. 2 and along the surface of theinsulating substrate may generate a tunneling current in multipledevices. This possible path is shown by dotted arrow 220. The surface ofthe insulating substrate along dotted arrow 220 may be substantiallyplanar. For example, the surfaces of the insulating substrate may notform part of a curved surface of a cylinder. By providing measurement bymultiple devices, the orientation of the devices shown in FIG. 2provides an improvement over conventional junction devices.

In addition to the improved orientation of the devices, embodiments mayinclude tapering the insulating layer, which may improve reliability,accuracy, and manufacturability. A tunneling junction for analyzing amolecule, such as DNA, may require an insulating layer with a thicknesson the order of nanometers (e.g., 1-2 nm). Current processingtechnologies for vertical layers may result in sidewall roughness orother variations that have the same order of magnitude as the thickness.In some areas, the insulating layer may be thinner than 1-2 nm and mayallow electrons to tunnel through, without the presence of a moleculecontacting the metal layers. Additionally, even if a thin, uniforminsulating layer of 1-2 nm can be fabricated, electrons may still tunnelfrom one metal layer to the other layer through the insulating layer,potentially across the entire surface area of the insulating layer.

This background tunneling current may make it difficult to detect when amolecule contacts the two metal layers. Tapering may allow the thicknessof the insulating layer to be the thickness preferred for a tunnelingjunction (e.g., on the order of nanometers) only near the point ofcontact with the molecule. The rest of the insulating layer may have athickness greater than the minimum thickness in areas other than at thepoint of contact. By tapering the insulating layer in this manner, thebackground tunneling current may be reduced. It is estimated that anadditional 1 Angstrom of thickness reduces tunneling current by an orderof magnitude. By tapering the insulating layer, the current fromelectrons tunneling through a molecule may be easier to detect when abackground current of electrons tunneling through the insulating layerexists. Tapering the insulating layer may also reduce junction shortingthrough pinhole and other defects. As a result, tapering can increasethe yield of a functioning device. Tapering can also effectively reducethe cross-sectional area of the junctions, thereby reducing themagnitude of tunneling current, and may make the structures moresuitable for molecular recognition. Some embodiments may not includetapering. For example, any of the figures included may not includetapering but may include a series or array of tunneling junctiondevices.

Such devices may allow for manufacturing methods that are improved overmethods for conventional tunneling junction devices. For example,embodiments may allow for certain fabrication steps to be performedunder vacuum without exposing the junctions to the atmosphere. Thejunction area may also not be exposed to photoresist andreactive-ion-etch processes that may lead to contamination and shorts.Such manufacturing methods may generate high density films, and thesehigh density films may allow fabrication of the thin junctions that arenanometer or sub-nanometer in size.

Accordingly, embodiments of the present technology may include tunnelingjunction devices that allow for a molecule to generate a tunnelingcurrent in multiple devices and allow for the tunneling current or otherelectrical characteristic to be measured reliably and repeatedly.Additional details of systems and methods are described below.

III. System of Devices

A. Arrays of Devices with Different Orientations of Tapering InsulatingMaterial

FIG. 3A shows a system 300 for analyzing a molecule according toembodiments of the present invention. System 300 includes a device 302,e.g., as part of a series of such devices. Device 302 includes a firstconductive element 304 and a second conductive element 306. Firstconductive element 304 may include a metal, and second conductiveelement 306 may include a metal. The metal may include a platinum groupmetal, including ruthenium, rhodium, palladium, osmium, iridium, orplatinum. In some embodiments, the metal may not oxidize in the presenceof water or air.

Device 302 may also include an insulating layer 308 tapered in adirection to reach a minimum thickness at a first end 314 of device 302.In FIG. 3A, the direction of the taper is parallel to an edge of firstconductive element 304, from the back side of device 302 hidden by theperspective in FIG. 3A to first end 314. Device 302 can be consideredlaterally tapered, instead of vertically tapered. As examples, theminimum thickness may be less than 1 nm, from 1 nm to 2 nm, from 2 nm to3 nm, from 3 nm to 4 nm, from 4 nm to 5 nm, or greater than 5 nm. Thetaper angle may be less than or equal to 5 degrees, from 5 degrees to 10degrees, from 10 degrees to 20 degrees, from 20 degrees to 30 degrees,from 30 degrees to 40 degrees, from 40 degrees to 45 degrees, from 45degrees to 50 degrees, or greater than 50 degrees. A line describing ataper has a slope, a rise over run. The taper angle is the arctangent ofthe slope. In other words, in FIG. 3A, the taper angle is half of theangle of the triangle formed by insulating layer 308 at the vertex atfirst end 314. Manufacturing processes and irregularities may result inthe absolute minimum thickness to be located close to but not exactly onthe first end. For example, the absolute minimum thickness may be withina 1 or 2 nm of the first end, or the thickness at the first end may bewithin 5% or 10% of the absolute minimum thickness of the insulatinglayer. As insulating layer 308 is disposed between first conductiveelement 304 and second conductive element 306, insulating layer 308 maycontact first conductive element 304 and second conductive element 306.The height of insulating layer 308 may be less than or equal to 100 nm.The area of the interface between the insulating layer 308 and aconductive element may be less than 10,000 nm². Insulating layer 308,first conductive element 304, and second conductive element 306 may eachhave a surface flush with the adjacent material (e.g., at least one ofconductive element 304, second conductive element 306, and insulatinglayer 308). The surface encompassing area 324 with the tunnelingjunction may be substantially flat.

Insulating layer 308 may be a dielectric. As examples, insulating layer308 may include any one or more of alumina (Al₂O₃), hafnia (HfO₂),silicon nitride (Si₃N₄), or silicon oxide (SiO₂). The insulatingmaterial may be a low-k dielectric material, which may allow for fasterreading of current changes. A low-k dielectric may have a dielectricconstant of less than or equal to 4.0, less than or equal to 3.9, lessthan or equal to 3.5, less than or equal to 3.0, less than or equal to2.5, less than or equal to 2.0, or less than or equal to 1.5. Theminimum thickness of the insulating layer may depend on the materialand/or the dielectric constant. For alumina, the minimum thickness canbe about 2 nm, which results in a tunneling current of about 100 pA. Theminimum thickness may also depend on the molecule to be analyzed. Theminimum thickness cannot be too large, otherwise the tunneling currentmay go through a portion of the molecule larger than the portion ofinterest (e.g., the tunneling current may pass through multiplenucleotides instead of a single nucleotide).

Device 302 further includes a voltage source 310 in electricalcommunication with first conductive element 304 and second conductiveelement 306. In addition, device 302 includes a current meter 312 inelectrical communication with voltage source 310, first conductiveelement 304, and second conductive element 306. As examples, voltagesource 310 may provide voltages from 0 to 1 V, including from 10 mV to100 mV, from 100 mV to 200 mV, from 200 mV to 300 mV, from 300 mV to 500mV, or from 500 mV to 1 V. In some embodiments, voltage source 210 mayprovide currents of 0 to 30 nA, including from 1 pA to 10 pA, from 10 pAto 100 pA, from 100 pA to 1 nA, 1 nA to 10 nA, or from 10 nA to 30 nA.As examples, voltage source 310 may supply a direct current voltage, analternating current voltage, or a different waveform (e.g., pulse, sine,square, triangle, or sawtooth). Although FIG. 3A shows multiple currentmeters, a single current meter may monitor individual currents for eachindividual device. Similarly, a single voltage source may supply voltageto a plurality of devices. In embodiments, the voltage source 310 may beconfigured to supply a fixed current and the voltage fluctuations aremeasured. In other embodiments, voltage source 310 may be configured tosupply a fixed voltage and the current fluctuations are measured.

Device 302 may include a tunneling direction that is orthogonal to thedirection of the taper. In other words, as viewed in FIG. 3A, thetunneling direction may be from left to right or from right to left. Thetunneling direction may be parallel to an axis 316 that passes throughfirst conductive element 304, second conductive element 306, andinsulating layer 308. System 300 may include a pair of electrodes 320powered by a power source 322 and configured to create an electric fieldin the tunneling direction. The electric field may drive the molecule tobe analyzed in the tunneling direction. In other embodiments, system 300may include an instrument configured to create a pressure-driven fluidflow in the tunneling direction. Such an instrument may include a pumpor an impeller for creating flow in the tunneling direction. The fluidcan be can be water or other suitable fluid for keeping the moleculesintact while allowing movement of the molecules across the tunnelingjunctions.

First conductive element 304, second conductive element 306, andinsulating layer 308 may be disposed on a surface of an insulatingsubstrate 318. As examples, insulating substrate 318 may be silicondioxide or an insulating material on top of a silicon wafer. As shown inFIG. 3A, the direction of the taper may be parallel to the surface ofthe insulating substrate. In particular, the direction of the taper isparallel to the surface of the insulating substrate while also beingorthogonal to a path of the molecule.

System 300 may include just one device 302 or may include a plurality ofdevices similar to device 302 in an array. The array may be configuredsuch that a molecule to be analyzed contacts a plurality of devices whendriven by an electric field or a pressure-driven fluid flow orthogonalto the direction of the taper. In FIG. 3A, the molecule can flow acrossthe array of devices 302 along path 326 so as to contact first end 314and the respective first ends of other devices in the array. In otherwords, the array would be arranged so that the molecule could move fromdevice to device when the molecule moves along a straight path. In someembodiments, the devices may be aligned so that the respective firstends of each device are along the same line. In other embodiments, thedevices may not lie on the same line, but may each be offset from a lineby the same distance so that the molecule may have to wind through thedevices (e.g., as described later with FIG. 5). To help with movement ofa molecule, an insulating material may be deposited between devices andpatterned to allow a molecule to move along a certain path. For example,a trench or channel may be formed with a sidewall of the trenchincluding the tunneling junction areas.

System 300 may include a device submerged in a liquid used inmicrofluidic applications. The liquid may facilitate flow of a molecule.The liquid may include water.

FIG. 3B shows a device 352 where the direction of the taper ofinsulating material 354 is orthogonal to the surface of an insulatingsubstrate 356 according to embodiments of the present invention. Thetaper in FIG. 3B can be considered vertically tapered. Insulatingmaterial 354 is between a first conductive element 358 and a secondconductive element 360. Insulating material 354 may be tapered to reacha minimum thickness at a first end of device 352. The first end ofdevice 352 is the side of device 352 that includes area 366. The end maybe at the top of device 352 or at an end farthest from insulatingsubstrate 356. Device 352 further includes a voltage source 362 and acurrent meter 364. Insulating material 354, insulating substrate 356,first conductive element 358, second conductive element 360, voltagesource 362, and current meter 364 may be any like component describedherein, including those described with FIG. 3A. With FIG. 3B, a moleculeto be analyzed would move either left to right or right to left (asviewed in FIG. 3B) over the top of the devices, making contact with thetop surfaces of one or more of the devices. Path 368 is a possible pathof a molecule to be analyzed. An additional insulating material may beadded to fill in the trenches between tunneling junction devices so thata molecule may travel over a substantially flat surface.

B. Devices without a Tapered Insulating Material

FIG. 4A and FIG. 4B show different views of device 400 without a taperedinsulating material according to embodiments of the present invention.FIG. 4A shows a top view, and FIG. 4B shows a cross-sectional view.Insulating material 402 is between a first conductive element 404 and asecond conductive element 406. The width (in the horizontal direction inFIG. 4A and FIG. 4B) of insulating material 402 may be kept short toreduce tunneling current and risk of defects without introducing ataper. First conductive element 404 and second conductive element 406may increase in width and size from the interface with insulatingmaterial 402. The final shape, as viewed from the top, may be abutterfly-like shape. The increased size of the conductive elements canreduce risk of the conductive elements delaminating from insulatingmaterial 402. The top surfaces of insulating material 402, firstconductive element 404, and second conductive element 406 may besubstantially planar with an insulating layer 408. Insulating layer 408may include an insulating substrate, which may be any substratedescribed herein, and a material deposited on top of the insulatingsubstrate. With the top surfaces of insulating material 402, firstconductive element 404, second conductive element 406, and insulatinglayer 408 substantially planar, a molecule can move and contact aplurality of devices along an even surface, reducing the probabilitythat the molecule may get stuck or delayed between devices. FIGS. 4A and4B show an orientation of the insulating layer that is rotated from theorientation for conventional tunneling junction devices in the magneticmedia industry in FIG. 1. In some embodiments, insulating material 402may be tapered as described herein.

C. Flow Path to Linearize Molecule

FIG. 5 shows a system 500 for analyzing a molecule illustrating flow ofa molecule according to embodiments of the present invention. System 500includes a first device 502. First device 502 may have a firstconductive element 504 and a second conductive element 506, where eachare tapered in the same direction as the direction of the taper of aninsulating layer 508. In FIG. 5, device 502 has a lateral taper not avertical taper. System 500 also includes a second device 510 identicalto first device 502.

First device 502 has a first end 512, where the insulating layer 508 isat a minimum thickness, and a second end 514 opposite first end 512.Second device 510 has a first end 516, where the insulating layer is ata minimum thickness, and a second end 518 opposite first end 516. Firstend 512 of first device 502 may be closer to first end 516 of seconddevice 510 than second end 514 of second device 510. Similarly, firstend 516 of second device 510 may be closer to first end 512 of firstdevice 502 than second end 514 of first device 502. The first ends maybe said to face each other even though they are not aligned along anaxis defined by the direction of the taper. The distance between thebetween first device 502 and second device 510 may be measured based onthe axis in the direction of the taper without considering distances ina direction perpendicular to that axis. No other device may be betweenfirst device 502 and second device 510. In some embodiments, insulatinglayer 508 may not be tapered.

At the second end of each device, first conductive element 504 andsecond conductive element 506 may not be separated by insulating layer508. Instead, first conductive element 504 and second conductive element506 may be separated by a gap of air, liquid, or other fluid instead ofa solid. In some embodiments, first conductive element 504 and secondconductive element 506 may be separated by a solid insulating materialdifferent from the material in insulating layer 508. Device 502 anddevice 510 may be sandwiched between an insulating substrate 520 and aninsulating surface 522. As examples, insulating surface 522 may be adielectric, such as silicon oxide, aluminum oxide, hafnium oxide, orsilicon nitride. First conductive element 504, second conductive element506, insulating layer 508, insulating substrate 520, and insulatingsurface 522 may include any material described herein. In someembodiments, first conductive element 504 and second conductive element506 may be separated by insulating layer 508 at the second end of eachdevice.

First device 502 may be characterized by a first plane throughinsulating layer 508. The first plane is not shown in its entirety inFIG. 5 to maintain clarity. The first plane may include dashed line 530and may be orthogonal to insulating substrate 520. The first plane mayintersect the insulating layer 508 and neither first conductive element504 nor second conductive element 506. A second plane orthogonal to thefirst plane may intersect a portion of device 516. The second plane isnot shown in its entirety in FIG. 5. The second plane may include dashedline 532 and may be orthogonal to insulating substrate 520. The secondplane may intersect the insulating layer and the conductive elements indevice 510. Second device 510 may be characterized by a third planethrough the insulating layer. The third plane is not shown in itsentirety in FIG. 5. The third plane may include dashed line 536 and maybe orthogonal to insulating substrate 520. The second plane includingdashed line 532 may be orthogonal to the third plane including dashedline 536.

FIG. 5 shows a third device 534. Third device 534 may be identical tofirst device 502. The second plane comprising dashed line 532 mayintersect a portion of third device 534 with the conductive elements andthe insulating layer.

FIG. 5 shows a possible path 524 for the flow of a linear molecule(e.g., DNA) through system 500, e.g., by going between device 502 anddevice 510. The flow of DNA may be driven by electrophoresis or apressure gradient. Path 524 can allow for the molecule to contactdevices and register a tunneling current or electrical characteristic inthe devices. The winding path may help keep the molecule from coiling upor from being snagged by a single device. Device 502 and device 510 maybe oriented close enough to each other to force the molecule to travelthrough the flow channel as a linear molecule. In this manner, device502 and device 510 can be manufactured to be separated by nanometers orless than a nanometer. Nanopores or arrays of nanopore devices withpores having sub-nanometer sizes may not be easily manufactured.Although FIG. 5 shows DNA flow, the flow can apply to other molecules tobe analyzed.

In other words, the devices may be configured such that they oppose eachother to form a flow channel through which the molecule moves in alinear form during an analysis operation. First device 502 and seconddevice 510 may be offset from each other and still overlap with eachother in one dimension. First device 502 and third device 534 may bealigned in at least one dimension. A plane including dashed line 538 maybe orthogonal to the plane comprising dashed line 530. The planeincluding dashed line 538 may intersect at least one of the firstconductive element 504, second conductive element 506, and insulatinglayer 508. As shown in FIG. 5, dashed line 538 intersects firstconductive element 504 and second conductive element 506. The planeincluding dashed line 538 may not intersect device 510.

Each device may include an electrical meter in electrical communicationwith the conductive elements of the device. Each device may include avoltage source in electrical communication with the conductive elementsof the device. Each device may have a separate voltage or source, or thesame voltage source may be in electrical communication with multipledevices.

In embodiments, a device or an array of devices may be controlled by acomputer. The computer may be any type of computing instrument includingor controlling test equipment (including voltmeters, current meters,etc.). The computer may include or be coupled to an input and an outputinstrument coupled to the devices discussed herein.

IV. Methods of Analyzing Molecules

FIG. 6 shows a method 600 of analyzing a molecule. As examples, themolecule may be a monomer, a biological polymer, a nucleic acid, or apolypeptide. Biological polymers may include carbohydrates andpolysaccharides. Polypeptides include proteins. Analyzing a molecule mayinclude identifying the molecule or identifying a portion of themolecule. With nucleic acids, analyzing the nucleic acid may includeidentifying nucleotides of a portion of the nucleic acid. Withpolypeptides, analyzing the polypeptide may include identifying aminoacids in the polypeptide. Analyzing a biological polymer may includeidentifying a monomer unit of the polymer.

At block 602, method 600 includes applying a voltage across a firstelectrode and a second electrode separated by an insulating layer.Examples of devices including these electrodes and the insulating aredescribed above. A power supply, including a voltage source, may applythe voltage. The power supply may be controlled by a computer system.

Method 600 may include moving the molecule to the first electrode andthe second electrode by electrophoresis or a pressure-driven flow.Electrophoresis may be induced by applying a voltage across a pair ofelectrodes as described herein. A pressure-driven flow may be by a pump,impeller, or other suitable instrument. Movement of the molecule may becontrolled in part by a computer, through control of electrodes or thepump or impeller.

At block 604, method 600 includes contacting the molecule to the firstelectrode and the second electrode across the insulating layer. Theinsulating layer can be tapered such that the end of the insulatinglayer closest to the molecule includes the minimum thickness of theinsulating layer. Such tapering is described above, e.g., with respectto FIGS. 3A, 3B, and 5.

At block 606, method 600 includes measuring an electrical characteristicthrough the first electrode and the second electrode. A change inelectrical characteristic may be determined relative to a backgroundelectrical characteristic. The electrical characteristic may be measuredby an electrical meter, which may take various forms, as will beappreciated by one skilled in the art. Electrical characteristicsinclude current, voltage, and any other characteristic described herein.The measurement may be received by a computer system.

At block 608, method 600 may include identifying a portion of themolecule based on the measured electrical characteristic. Identifying aportion of the molecule may include identifying the presence or absenceof a part of a sequence of the molecule (e.g., a nucleotide or an aminoacid) or a functional group. Identifying the portion of the molecule mayinclude comparing the measured electrical characteristic or change inelectrical characteristic against a reference value or a calibrationvalue. The electrical characteristic may be current, voltage, or anycharacteristic described herein. For example, each of the fournucleotides of DNA or each of the 20 amino acids of proteins may have acurrent or change in current previously characterized. Distinguishingdifferent portions of the molecule may use current differences on theorder of tens of picoamps. The calibration current or reference currentmay be based on a plurality of readings. For example, the referencecurrent may be based on hundreds, thousands, or tens of thousands ofcurrent measurements across the device or similar devices. Such measuredvalues can be averaged, and the average can be compared to a referenceor calibration value. Other statistical values besides a mean averagecan be used, e.g., a median or mode. Identification of the portion ofthe molecule may use a computer system. The computer system may havereference currents or other electrical characteristics stored within thesystem.

Method 600 may include a second tunneling junction device, e.g., as partof an array of devices, as mentioned above. Method 600 may includeapplying a voltage across a third electrode and a fourth electrode,which are separated by a second insulating layer. Method 600 may furtherinclude moving the molecule from the first electrode and the secondelectrode to the third electrode and the fourth electrode. In addition,method 600 may include contacting the molecule to the third electrodeand the fourth electrode across the second insulating layer. The secondinsulating layer may be tapered such that the second insulating layer isat a minimum thickness at the end of the second insulating layer closestto the molecule. Method 600 may include measuring an electricalcharacteristic through the third electrode and the fourth electrode.

Method 600 may further include comparing the electrical characteristicthrough the third electrode and the fourth electrode to the electricalcharacteristic through the first electrode and the second electrode.Comparing the electrical characteristics may include averagingelectrical characteristic values (average may include mean, median, ormode), performing other statistical functions (e.g., calculatingstandard deviation, t-test), or plotting the current values. Comparingthe electrical characteristic may use a computer system. Method 600 mayinclude contacting the molecule to a plurality of devices. The pluralitymay include from 50 to 100, from 100 to 500, from 500 to 1,000, from1,000 to 5,000, from 5,000 to 10,000, or over 10,000 devices. Astatistical test may be used to determine if the electricalcharacteristic distribution from a portion of the molecule is the sameor different from reference electrical characteristic.

In some embodiments, methods may include flowing a molecule through aflowpath formed by offset and overlapping devices as described hereinwith FIG. 5.

V. Methods of Manufacturing

FIG. 7 shows a method 700 of manufacturing a device for analyzing amolecule. Manufacturing methods may include techniques used withmanufacturing magnetic recording media (e.g., magnetic hard drives).

At block 702, method 700 includes depositing a first conductive elementon a surface of an insulating substrate. The first conductive elementmay be deposited by ion beam deposition. Ion beam deposition may resultin a denser film compared to other techniques. The first conductiveelement may be patterned to the target dimensions by suitable patterningtechniques.

At block 704, method 700 includes depositing an insulating layer on thesidewall of the first conductive element. The insulating layer may bedeposited by ion beam deposition (IBD) or atomic layer deposition (ALD).The insulating layer may be deposited conformally over the firstconductive element.

At block 706, method 700 includes tapering the insulating layer on thesidewall of the first conductive element to form a tapered insulatinglayer. Tapering the insulating layer may include tapering the insulatinglayer in a direction orthogonal to the surface of the insulatingsubstrate (i.e., a vertical taper). In other embodiments, tapering theinsulating layer may include tapering the insulating layer in adirection parallel to the surface of the insulating substrate (i.e., alateral taper). Tapering the insulating layer may include ion beametching of the insulating layer at an angle (e.g., ion beam with argonions at a 45 degree angle). The tapering may be aided by shadowing ofthe sidewall provided by the adjacent feature patterned in the firstconductive element. For example, the adjacent feature may form a trenchwith the sidewall of the first conductive element, and the trench mayshadow part of the insulating layer on the sidewall to aid in tapering.

In some embodiments, depositing the insulating layer may be shadowed byanother structure, and the insulating layer as deposited may be taperedinstead of conformal over the first conductive element. As a result, themethod may reduce the tapering through an etching operation or themethod may eliminate the tapering operation entirely.

At block 706, method 700 include depositing a second conductive elementcontacting the tapered insulating layer. The second conductive elementmay be deposited with IBD or ALD.

At block 710, method 700 includes planarizing at least one of the firstconductive element or the second conductive element to expose thetapered insulating layer. Planarizing may be by chemical mechanicalplanarization or ion beam etching.

Method 700 may further include connecting the first conductive elementand the second conductive element to a voltage source and an electricalmeter. Electrically connecting the first conductive element and thesecond conductive element to the voltage source or electrical meter mayinclude metal pads or contacts and other metal processing techniquesknown in magnetic recording media manufacturing.

A. Example Method of Forming Vertical Taper

FIG. 8A shows an example of forming a vertically tapered tunnelingjunction device. In section 801, an adhesion layer, a metal, and a hardmask are deposited by ion beam deposition (IBD). The adhesion layer isdeposited on top of SiO₂ or Si. The metal (e.g., platinum or palladium)is deposited on top of the adhesion layer. The hard mask is deposited ontop of the metal. In section 802, junctions are patterned withphotolithography, hard-mask reactive ion etch (RIE), and resist removal.In section 803, ion beam etching (IBE) is done to mill the metal and tosmooth sidewalls. In section 804, a dielectric layer is deposited by ionbeam deposition (IBD) or atomic layer deposition (IBD). In section 805,the dielectric on the sidewalls is tapered using IBE and a shadowingeffect.

FIG. 8B shows additional detail on tapering in section 805 andadditional steps in processing, following FIG. 8A. Structure 82 may beused to shadow structure 81. The structure used to shadow the sidewallmay be aligned with the structure having sidewall targeted to betapered. A flux of ions, including those from argon, may be introducedat an angle non-normal and non-parallel relative to the surface of thesubstrate. The flux of ions may be swept in the XZ plane (direction) tocreate the thickness gradient. Some of the ions are blocked by structure82 before the ions reach the sidewall of structure 81. More ions thatwould otherwise be headed toward the bottom of structure 81 are blockedthan ions that are headed to toward the top of structure 81. As aresult, more of the dielectric is etched away from the top of structure81 compared to the bottom of structure 81, resulting in a taper in thedielectric. In section 806, a metal is deposited by IBD or ALD. Thismetal may eventually form the second electrode of the device. In section807, IBE or chemical mechanical planarization (CMP) is used to exposethe minimum thickness of the tapered dielectric.

B. Example Method of Forming Lateral Taper

FIG. 9A shows an example of forming a laterally tapered tunnelingjunction device. In section 901, an adhesion layer, a metal, and a hardmask are deposited by ion beam deposition (IBD). The adhesion layer isdeposited on top of SiO₂ or Si. The metal (e.g., platinum or palladium)is deposited on top of the adhesion layer. The hard mask is deposited ontop of the metal. In section 902, junctions are patterned withphotolithography, hard-mask reactive ion etch (RIE), and resist removal.In section 903, ion beam etching (IBE) is done to mill the metal and tosmooth sidewalls. In section 904, dielectric layer is deposited by ionbeam deposition (IBD) or atomic layer deposition (IBD). In section 905,the dielectric on the sidewalls is tapered using IBE and a shadowingeffect.

FIG. 9B shows additional detail on tapering in section 905 andadditional steps in processing, following FIG. 9A. The argon flux angleand the shadowing is different from FIG. 9B. To create a lateral taper,a structure offset from the sidewall to be tapered is used forshadowing, while in FIG. 8B, the structure used for shadowing is alignedto the sidewall. In FIG. 9B, structure 92 is offset from structure 91and shadows structure 91. A flux of ions, including those from argon,may be introduced at an angle ϕ that may be non-normal or non-parallelrelative to the surface of the substrate. The ions may be swept in theXY plane to create the thickness gradient. Some of the ions are blockedby structure 92 before the ions reach the sidewall at one end ofstructure 91 closest to the center of mass of structure 92. More ionsthat would otherwise be headed toward the end of structure 91 areblocked than ions that are headed to toward structure 91 but fartherfrom the end. As a result, more of the dielectric is etched away fromthe end of structure 91, resulting in a taper in the dielectric. Insection 906, a metal is deposited by IBD or ALD. This metal mayeventually form the second electrode of the device. In section 907, IBEor chemical mechanical planarization (CMP) is used to expose the minimumthickness of the tapered dielectric.

VI. Computer System

Any of the computer systems mentioned herein may utilize any suitablenumber of subsystems. Examples of such subsystems are shown in FIG. 10in computer system 10. In some embodiments, a computer system includes asingle computer apparatus, where the subsystems can be the components ofthe computer apparatus. In other embodiments, a computer system caninclude multiple computer apparatuses, each being a subsystem, withinternal components. A computer system can include desktop and laptopcomputers, tablets, mobile phones and other mobile devices.

The subsystems shown in FIG. 10 are interconnected via a system bus 75.Additional subsystems such as a printer 74, keyboard 78, storagedevice(s) 79, monitor 76, which is coupled to display adapter 82, andothers are shown. Peripherals and input/output (I/O) devices, whichcouple to I/O controller 71, can be connected to the computer system byany number of means known in the art such as input/output (I/O) port 77(e.g., USB, FireWire®, Thunderbolt). For example, I/O port 77 orexternal interface 81 (e.g. Ethernet, Wi-Fi, etc.) can be used toconnect computer system 10 to a wide area network such as the Internet,a mouse input device, or a scanner. The interconnection via system bus75 allows the central processor 73 to communicate with each subsystemand to control the execution of instructions from system memory 72 orthe storage device(s) 79 (e.g., a fixed disk, such as a hard drive, oroptical disk), as well as the exchange of information betweensubsystems. The system memory 72 and/or the storage device(s) 79 mayembody a computer readable medium. Another subsystem is a datacollection device 85, such as a camera, microphone, accelerometer, andthe like. Any of the data mentioned herein can be output from onecomponent to another component and can be output to the user.

A computer system can include a plurality of the same components orsubsystems, e.g., connected together by external interface 81 or by aninternal interface. In some embodiments, computer systems, subsystem, orapparatuses can communicate over a network. In such instances, onecomputer can be considered a client and another computer a server, whereeach can be part of a same computer system. A client and a server caneach include multiple systems, subsystems, or components.

It should be understood that any of the embodiments of the presentinvention can be implemented in the form of control logic using hardware(e.g. an application specific integrated circuit or field programmablegate array) and/or using computer software with a generally programmableprocessor in a modular or integrated manner. As used herein, a processorincludes a single-core processor, multi-core processor on a sameintegrated chip, or multiple processing units on a single circuit boardor networked. Based on the disclosure and teachings provided herein, aperson of ordinary skill in the art will know and appreciate other waysand/or methods to implement embodiments of the present invention usinghardware and a combination of hardware and software.

Any of the software components or functions described in thisapplication may be implemented as software code to be executed by aprocessor using any suitable computer language such as, for example,Java, C, C++, C #, Objective-C, Swift, or scripting language such asPerl or Python using, for example, conventional or object-orientedtechniques. The software code may be stored as a series of instructionsor commands on a computer readable medium for storage and/ortransmission. A suitable non-transitory computer readable medium caninclude random access memory (RAM), a read only memory (ROM), a magneticmedium such as a hard-drive or a floppy disk, or an optical medium suchas a compact disk (CD) or DVD (digital versatile disk), flash memory,and the like. The computer readable medium may be any combination ofsuch storage or transmission devices.

Such programs may also be encoded and transmitted using carrier signalsadapted for transmission via wired, optical, and/or wireless networksconforming to a variety of protocols, including the Internet. As such, acomputer readable medium according to an embodiment of the presentinvention may be created using a data signal encoded with such programs.Computer readable media encoded with the program code may be packagedwith a compatible device or provided separately from other devices(e.g., via Internet download). Any such computer readable medium mayreside on or within a single computer product (e.g. a hard drive, a CD,or an entire computer system), and may be present on or within differentcomputer products within a system or network. A computer system mayinclude a monitor, printer, or other suitable display for providing anyof the results mentioned herein to a user.

Any of the methods described herein may be totally or partiallyperformed with a computer system including one or more processors, whichcan be configured to perform the steps. Thus, embodiments can bedirected to computer systems configured to perform the steps of any ofthe methods described herein, potentially with different componentsperforming a respective steps or a respective group of steps. Althoughpresented as numbered steps, steps of methods herein can be performed ata same time or in a different order. Additionally, portions of thesesteps may be used with portions of other steps from other methods. Also,all or portions of a step may be optional. Additionally, any of thesteps of any of the methods can be performed with modules, units,circuits, or other means for performing these steps.

FIG. 11 shows an exemplary analysis system. The system depicted in FIG.11 comprises an analysis device 1102 and an intelligence module 1104which is part of the computer system 1106. Analysis device 1102 mayinclude system 200, system 300, system 350, device 400, system 500, orany system described herein. Computer system 1106 may include parts orall of computer system 10. The data sets (electrical characteristicsdata sets) are transferred from the analysis device 1102 to theintelligence module 1104 or vice versa via a network connection or adirect connection. The data sets may for example be processed toidentify nucleotides. The identification steps may be implemented bysoftware stored on the hardware of computer system 1106. The data setsmay be processed by computer code running on the processor and beingstored on the storage device of the intelligence module and afterprocessing transferred back to the storage device of the analysismodule, where the modified data may be displayed on a displaying device.In some embodiments, the intelligence module may also be implemented inthe analysis device.

FIG. 12 shows that computer system 1200 may comprise receiving means1210, which may include, for example, receiving electricalcharacteristic data obtained from a sequencing device. Computer system1200 may also include identifying means 1220 for identifying a portionof a molecule causing a change in the electrical characteristic in thedata.

The specific details of particular embodiments may be combined in anysuitable manner without departing from the spirit and scope ofembodiments of the invention. However, other embodiments of theinvention may be directed to specific embodiments relating to eachindividual aspect, or specific combinations of these individual aspects.

The above description of example embodiments of the invention has beenpresented for the purposes of illustration and description. It is notintended to be exhaustive or to limit the invention to the precise formdescribed, and many modifications and variations are possible in lightof the teaching above.

In the preceding description, for the purposes of explanation, numerousdetails have been set forth in order to provide an understanding ofvarious embodiments of the present technology. It will be apparent toone skilled in the art, however, that certain embodiments may bepracticed without some of these details, or with additional details.

Having described several embodiments, it will be recognized by those ofskill in the art that various modifications, alternative constructions,and equivalents may be used without departing from the spirit of theinvention. Additionally, a number of well-known processes and elementshave not been described in order to avoid unnecessarily obscuring thepresent invention. Additionally, details of any specific embodiment maynot always be present in variations of that embodiment or may be addedto other embodiments.

Where a range of values is provided, it is understood that eachintervening value, to the tenth of the unit of the lower limit unlessthe context clearly dictates otherwise, between the upper and lowerlimits of that range is also specifically disclosed. Each smaller rangebetween any stated value or intervening value in a stated range and anyother stated or intervening value in that stated range is encompassed.The upper and lower limits of these smaller ranges may independently beincluded or excluded in the range, and each range where either, neither,or both limits are included in the smaller ranges is also encompassedwithin the invention, subject to any specifically excluded limit in thestated range. Where the stated range includes one or both of the limits,ranges excluding either or both of those included limits are alsoincluded.

As used herein and in the appended claims, the singular forms “a”, “an”,and “the” include plural referents unless the context clearly dictatesotherwise. Thus, for example, reference to “a method” includes aplurality of such methods and reference to “the particle” includesreference to one or more particles and equivalents thereof known tothose skilled in the art, and so forth. The invention has now beendescribed in detail for the purposes of clarity and understanding.However, it will be appreciated that certain changes and modificationsmay be practice within the scope of the appended claims.

All publications, patents, and patent applications cited herein arehereby incorporated by reference in their entirety for all purposes.None is admitted to be prior art.

What is claimed is:
 1. A system for analyzing a molecule, the systemcomprising a device, the device comprising: a first conductive element;a second conductive element; an insulating layer tapered in a directionto reach a minimum thickness at a first end of the device, theinsulating layer disposed between the first conductive element and thesecond conductive element; a voltage source in electrical communicationwith the first conductive element and the second conductive element; andan electrical meter in electrical communication with the voltage source,the first conductive element, and the second conductive element.
 2. Thesystem of claim 1, wherein: the direction is a first direction, furthercomprising: a pair of electrodes configured to create an electric fieldin a second direction orthogonal to the first direction, wherein thesecond direction is parallel to an axis that passes through the firstconductive element, and the insulating layer.
 3. The system of claim 1,wherein: the direction is a first direction, further comprising: aninstrument configured to create a pressure-driven fluid flow in a seconddirection orthogonal to the first direction, wherein the seconddirection is parallel to an axis that passes through the firstconductive element, the insulating layer, and the second conductiveelement.
 4. The system of claim 1, wherein the first conductive elementcomprises a metal, the second conductive element comprises a metal, andthe insulating layer is a dielectric.
 5. The system of claim 1, whereinthe insulating layer comprises alumina, hafnia, silicon nitride, orsilicon oxide.
 6. The system of claim 1, wherein: the first conductiveelement, the second conductive element, and the insulating layer aredisposed on a surface of an insulating substrate, and the direction isorthogonal to the surface of the insulating substrate.
 7. The system ofclaim 1, wherein: the first conductive element, the second conductiveelement, and the insulating layer are disposed on a surface of aninsulating substrate, and the direction is parallel to the surface ofthe insulating substrate.
 8. The system of claim 1, further comprising aplurality of devices in an array that includes the device.
 9. The systemof claim 8, wherein the array is configured such that the moleculecontacts the plurality of devices when driven by an electric field or apressure-driven fluid flow orthogonal to the direction.
 10. The systemof claim 1, wherein: the device is a first device, the system comprisesa second device identical to the first device, the first devicecomprises a second end opposite the first end of the first device, thesecond device comprises a second end opposite the first end of thesecond device, and the first device and the second device are disposedon a surface of an insulating substrate such that: the first end of thefirst device is closer to the first end of the second device than thesecond end of the second device, and the first end of the second deviceis closer to the first end of the first device than the second end ofthe first device.
 11. The system of claim 1, wherein: the firstconductive element and the second conductive element are each taperedsuch that the maximum thickness of each element is not at the first end,the first conductive element and the second conductive element are notseparated by the insulating layer at a second end opposite the firstend.
 12. The system of claim 1, further comprising a liquid, wherein aportion of the device is submerged in the liquid.